There is something not quite right here. <div><br></div><div>I grompp a gro file created from a pdb file using pdb2gmx and run MD to do a single point energy calculation. </div><div><br></div><div>I then grompp the original pdb file and run MD to do a single point energy calculation.</div>
<div><br></div><div>The values of potential energy values are different by about 3 kJ/mol for a small molecule. </div><div><br></div><div>These things should carry a "bad for your health" sign :D</div>